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Conserved domains on  [gi|1268119045|ref|WP_098679031|]
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MULTISPECIES: DUF3967 domain-containing protein [Bacillus cereus group]

Protein Classification

HTH_MerR-SF and DUF3967 domain-containing protein( domain architecture ID 10249018)

HTH_MerR-SF and DUF3967 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_MerR-SF super family cl02600
Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; ...
 10-91 1.12e-06

Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily; Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.


The actual alignment was detected with superfamily member cd04765:

Pssm-ID: 470628  Cd Length: 99  Bit Score: 44.94  E-value: 1.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268119045  10 DVAERLEIGTSTLRKWcialEQE--QYSFVKGAKNSRAFVQKDIKVLEQMKKLIQEAGMSIEGAVKVVLSVPFAEVETDN 87
Cdd:cd04765     5 EVAEILGLPPHVLRYW----ETEfpQLKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEE 80


                  ....
gi 1268119045  88 DLED 91
Cdd:cd04765    81 AEER 84
DUF3967 pfam13152
Protein of unknown function (DUF3967); This family of proteins is functionally uncharacterized. ...
 145-183 1.33e-04

Protein of unknown function (DUF3967); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 173 and 249 amino acids in length.


:

Pssm-ID: 289896  Cd Length: 35  Bit Score: 37.85  E-value: 1.33e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1268119045 145 RYNERDNLLLTHVREIQETKQLLVASQnkqkEKKWWEFW 183
Cdd:pfam13152   1 RLENRDEQLMQVIREIQETKRLIAASQ----QKKWWQFW 35
PLN03137 super family cl33645
ATP-dependent DNA helicase; Q4-like; Provisional
 99-138 3.35e-03

ATP-dependent DNA helicase; Q4-like; Provisional


The actual alignment was detected with superfamily member PLN03137:

Pssm-ID: 215597 [Multi-domain]  Cd Length: 1195  Bit Score: 37.57  E-value: 3.35e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1268119045   99 LSENVMNLPKEFIEQLLQEQILLKEKIQQLErIEIMNAER 138
Cdd:PLN03137   307 LLDNAADLSPDQVEQLRQDRLQLKKQIQQLE-IHIRDKER 345
 
Name Accession Description Interval E-value
HTH_MlrA-like_sg2 cd04765
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 10-91 1.12e-06

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133393  Cd Length: 99  Bit Score: 44.94  E-value: 1.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268119045  10 DVAERLEIGTSTLRKWcialEQE--QYSFVKGAKNSRAFVQKDIKVLEQMKKLIQEAGMSIEGAVKVVLSVPFAEVETDN 87
Cdd:cd04765     5 EVAEILGLPPHVLRYW----ETEfpQLKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEE 80


                  ....
gi 1268119045  88 DLED 91
Cdd:cd04765    81 AEER 84
DUF3967 pfam13152
Protein of unknown function (DUF3967); This family of proteins is functionally uncharacterized. ...
 145-183 1.33e-04

Protein of unknown function (DUF3967); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 173 and 249 amino acids in length.


Pssm-ID: 289896  Cd Length: 35  Bit Score: 37.85  E-value: 1.33e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1268119045 145 RYNERDNLLLTHVREIQETKQLLVASQnkqkEKKWWEFW 183
Cdd:pfam13152   1 RLENRDEQLMQVIREIQETKRLIAASQ----QKKWWQFW 35
PLN03137 PLN03137
ATP-dependent DNA helicase; Q4-like; Provisional
 99-138 3.35e-03

ATP-dependent DNA helicase; Q4-like; Provisional


Pssm-ID: 215597 [Multi-domain]  Cd Length: 1195  Bit Score: 37.57  E-value: 3.35e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1268119045   99 LSENVMNLPKEFIEQLLQEQILLKEKIQQLErIEIMNAER 138
Cdd:PLN03137   307 LLDNAADLSPDQVEQLRQDRLQLKKQIQQLE-IHIRDKER 345
MerR_1 pfam13411
MerR HTH family regulatory protein;
9-74 8.62e-03

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 33.68  E-value: 8.62e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1268119045   9 KDVAERLEIGTSTLRKWciaLEQEQYSFVKGAKNSRAFVQKDIKVLEQMKKLiQEAGMSIEGAVKV 74
Cdd:pfam13411   4 SELARLLGVTPRTLRYW---EREGLLPPPRTERGRRYYTDEDVERLRLIKAL-LERGLSLKEIKEL 65
 
Name Accession Description Interval E-value
HTH_MlrA-like_sg2 cd04765
Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative ...
 10-91 1.12e-06

Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators; Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.


Pssm-ID: 133393  Cd Length: 99  Bit Score: 44.94  E-value: 1.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1268119045  10 DVAERLEIGTSTLRKWcialEQE--QYSFVKGAKNSRAFVQKDIKVLEQMKKLIQEAGMSIEGAVKVVLSVPFAEVETDN 87
Cdd:cd04765     5 EVAEILGLPPHVLRYW----ETEfpQLKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEE 80


                  ....
gi 1268119045  88 DLED 91
Cdd:cd04765    81 AEER 84
DUF3967 pfam13152
Protein of unknown function (DUF3967); This family of proteins is functionally uncharacterized. ...
 145-183 1.33e-04

Protein of unknown function (DUF3967); This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 173 and 249 amino acids in length.


Pssm-ID: 289896  Cd Length: 35  Bit Score: 37.85  E-value: 1.33e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1268119045 145 RYNERDNLLLTHVREIQETKQLLVASQnkqkEKKWWEFW 183
Cdd:pfam13152   1 RLENRDEQLMQVIREIQETKRLIAASQ----QKKWWQFW 35
HTH_MlrA-CarA cd01104
Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; ...
 8-76 1.11e-03

Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA; Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.


Pssm-ID: 133379  Cd Length: 68  Bit Score: 36.06  E-value: 1.11e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1268119045   8 TKDVAERLEIGTSTLRKWcialeQEQYSFVK---GAKNSRAFVQKDIKVLEQMKKLIQEaGMSIEGAVKVVL 76
Cdd:cd01104     3 IGAVARLTGVSPDTLRAW-----ERRYGLPApqrTDGGHRLYSEADVARLRLIRRLTSE-GVRISQAAALAL 68
PLN03137 PLN03137
ATP-dependent DNA helicase; Q4-like; Provisional
 99-138 3.35e-03

ATP-dependent DNA helicase; Q4-like; Provisional


Pssm-ID: 215597 [Multi-domain]  Cd Length: 1195  Bit Score: 37.57  E-value: 3.35e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|
gi 1268119045   99 LSENVMNLPKEFIEQLLQEQILLKEKIQQLErIEIMNAER 138
Cdd:PLN03137   307 LLDNAADLSPDQVEQLRQDRLQLKKQIQQLE-IHIRDKER 345
MerR_1 pfam13411
MerR HTH family regulatory protein;
9-74 8.62e-03

MerR HTH family regulatory protein;


Pssm-ID: 463870  Cd Length: 66  Bit Score: 33.68  E-value: 8.62e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1268119045   9 KDVAERLEIGTSTLRKWciaLEQEQYSFVKGAKNSRAFVQKDIKVLEQMKKLiQEAGMSIEGAVKV 74
Cdd:pfam13411   4 SELARLLGVTPRTLRYW---EREGLLPPPRTERGRRYYTDEDVERLRLIKAL-LERGLSLKEIKEL 65
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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